Genome-wide R-loop Landscapes during Cell Differentiation and Reprogramming Article Swipe

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Pengze Yan , Zunpeng Liu , Moshi Song , Zeming Wu , Wei Xu , Kuan Li , Qianzhao Ji , Si Wang , Xiaoqian Liu , Kaowen Yan , Concepción Rodrı́guez Esteban , Weimin Ci , Juan Carlos Izpisúa Belmonte , Wei Xie , Jie Ren , Weiqi Zhang , Qianwen Sun , Jing Qu , Guang‐Hui Liu ·

YOU? · · 2020 · Open Access · · DOI: https://doi.org/10.1016/j.celrep.2020.107870

DNA:RNA hybrids play key roles in both physiological and disease states by regulating chromatin and genome organization. Their homeostasis during cell differentiation and cell plasticity remains elusive. Using an isogenic human stem cell platform, we systematically characterize R-loops, DNA methylation, histone modifications, and chromatin accessibility in pluripotent cells and their lineage-differentiated derivatives. We confirm that a portion of R-loops formed co-transcriptionally at pluripotency genes in pluripotent stem cells and at lineage-controlling genes in differentiated lineages. Notably, a subset of R-loops maintained after differentiation are associated with repressive chromatin marks on silent pluripotency genes and undesired lineage genes. Moreover, in reprogrammed pluripotent cells, cell-of-origin-specific R-loops are initially present but are resolved with serial passaging. Our analysis suggests a multifaceted role of R-loops in cell fate determination that may serve as an additional layer of modulation on cell fate memory and cell plasticity.

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Reprogramming Biology Induced pluripotent stem cell Chromatin Cellular differentiation Cell biology Lineage (genetic) Cell fate determination Histone Epigenetics Genetics Gene Embryonic stem cell Transcription factor

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Type: article
Language: en
Landing Page: https://doi.org/10.1016/j.celrep.2020.107870
PDF: http://www.cell.com/article/S2211124720308512/pdf
OA Status: gold
Cited By: 71
References: 110
Related Works: 10
OpenAlex ID: https://openalex.org/W3040828226

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OpenAlex ID: https://openalex.org/W3040828226

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DOI: https://doi.org/10.1016/j.celrep.2020.107870

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Title: Genome-wide R-loop Landscapes during Cell Differentiation and Reprogramming

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Type: article

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Language: en

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Publication year: 2020

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Publication date: 2020-07-01

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Authors: Pengze Yan, Zunpeng Liu, Moshi Song, Zeming Wu, Wei Xu, Kuan Li, Qianzhao Ji, Si Wang, Xiaoqian Liu, Kaowen Yan, Concepción Rodrı́guez Esteban, Weimin Ci, Juan Carlos Izpisúa Belmonte, Wei Xie, Jie Ren, Weiqi Zhang, Qianwen Sun, Jing Qu, Guang‐Hui Liu

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Landing page: https://doi.org/10.1016/j.celrep.2020.107870

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PDF URL: https://www.cell.com/article/S2211124720308512/pdf

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OA status: gold

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OA URL: https://www.cell.com/article/S2211124720308512/pdf

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Concepts: Reprogramming, Biology, Induced pluripotent stem cell, Chromatin, Cellular differentiation, Cell biology, Lineage (genetic), Cell fate determination, Histone, Epigenetics, Genetics, Gene, Embryonic stem cell, Transcription factor

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Cited by: 71

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Citations by year (recent): 2025: 12, 2024: 9, 2023: 14, 2022: 18, 2021: 15

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References (count): 110

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Related works (count): 10

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